modify clinvar star assignment for no interpretation variants #139
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
naqvia
reviewed
Aug 22, 2023
| @@ -419,7 +419,7 @@ master_tab <- master_tab %>% | |||
| evidenceBP = coalesce(as.double(evidenceBP.x, evidenceBP.y)), | |||
| Intervar_evidence = coalesce(`InterVar: InterVar and Evidence.x`, `InterVar: InterVar and Evidence.y`), | |||
| # replace second final call with the second one because we did not use interVar results | |||
| final_call.x = if_else(Stars == "0", final_call.y, final_call.x) | |||
| final_call.x = if_else(Stars == "0" | is.na(Stars), final_call.y, final_call.x) | |||
naqvia
approved these changes
Aug 22, 2023
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Purpose/implementation Section
What feature is being added or bug is being addressed?
Closes #138. This PR assigns ClinVar variants with
no_interpretation_for_single_variantas zero starsWhat was your approach?
What GitHub issue does your pull request address?
#138
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Please check new code logic.
Is there anything that you want to discuss further?
I also updated another line of code where final calls are chosen based on whether clinVar or intervar was used. Before it was only taking intervar calls when Stars == 0, but should now also consider variants with NA stars.
Documentation Checklist